Hi Flynn,
When you’re running Klipper, the Pi itself becomes the “brain” of the operation, your motherboard becomes just a driver for the motors and sensors. When my octopus wasn’t relegated to a desk ornament I had run into a similar issue that you had, I found that rather than going with the path that BigTreeTech has listed on their website I instead ran USB to my U2C and a separate line to the motherboard (diagram below)
